{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/1519","repository_url":"https://api.github.com/repos/biocore/scikit-bio","labels_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1519/labels{/name}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1519/comments","events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1519/events","html_url":"https://github.com/biocore/scikit-bio/issues/1519","id":239142145,"number":1519,"title":"RDA fails for non-test datasets","user":{"login":"stevendbrown","id":7763249,"avatar_url":"https://avatars2.githubusercontent.com/u/7763249?v=4","gravatar_id":"","url":"https://api.github.com/users/stevendbrown","html_url":"https://github.com/stevendbrown","followers_url":"https://api.github.com/users/stevendbrown/followers","following_url":"https://api.github.com/users/stevendbrown/following{/other_user}","gists_url":"https://api.github.com/users/stevendbrown/gists{/gist_id}","starred_url":"https://api.github.com/users/stevendbrown/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stevendbrown/subscriptions","organizations_url":"https://api.github.com/users/stevendbrown/orgs","repos_url":"https://api.github.com/users/stevendbrown/repos","events_url":"https://api.github.com/users/stevendbrown/events{/privacy}","received_events_url":"https://api.github.com/users/stevendbrown/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-06-28T12:05:01Z","updated_at":"2017-08-19T02:30:46Z","closed_at":null,"body":"Running `skbio.stats.ordination.RDA` on an experimental dataset where `y.shape` is (154, 1369) and `x.shape` is (154, 1), I get the following error:\r\n\r\n`ValueError: Shape of passed values is (154, 1), indices imply (153, 1)`\r\n\r\nwhich is triggered by:\r\n\r\nhttps://github.com/biocore/scikit-bio/blob/master/skbio/stats/ordination/_redundancy_analysis.py#L211\r\n\r\nI haven't figured out why this was causing a problem for my data case but not for the test data; obviously there's a shape mismatch in `pc_ids` and the `biplot_scores` which exists before line 211 but where that comes from I don't yet know.\r\n\r\nIf I regress `biplot_scores` to `biplot_scores = pd.DataFrame(biplot_scores)` then I get \"correct-looking\" results (as in the data are beautifully separated per experimental design), but the module then fails build tests. I started getting my hands dirty in the testing code but got caught up in firefighting at the wetlab bench before I could figure it out. Is there an online version of Legendre & Legendre I can read?"},"comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments/323494492","html_url":"https://github.com/biocore/scikit-bio/issues/1519#issuecomment-323494492","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1519","id":323494492,"user":{"login":"essicolo","id":5118227,"avatar_url":"https://avatars3.githubusercontent.com/u/5118227?v=4","gravatar_id":"","url":"https://api.github.com/users/essicolo","html_url":"https://github.com/essicolo","followers_url":"https://api.github.com/users/essicolo/followers","following_url":"https://api.github.com/users/essicolo/following{/other_user}","gists_url":"https://api.github.com/users/essicolo/gists{/gist_id}","starred_url":"https://api.github.com/users/essicolo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/essicolo/subscriptions","organizations_url":"https://api.github.com/users/essicolo/orgs","repos_url":"https://api.github.com/users/essicolo/repos","events_url":"https://api.github.com/users/essicolo/events{/privacy}","received_events_url":"https://api.github.com/users/essicolo/received_events","type":"User","site_admin":false},"created_at":"2017-08-19T02:30:46Z","updated_at":"2017-08-19T02:30:46Z","body":"I'd do it, but\r\n1) I already have a pending PR and don't know how to create a second one. \r\n2) I'm not sure if residual columns should be named RDA. The R vegan package name them PC."}}
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